I have such tool in my personal use, not limited to NES and small pictures, but it is so user unfriendly so even I have difficulties with it. If you won't be able to find something better, I can fix it a bit to be more useful for users other than me.

Pyxel EditIt can do everything in your list. (though the way it saves an array to a file may not be best for you. But whatever)Import an image with 8x8 tile size. It will check for duplicates, even transformations. (Sadly you can't choose which transformations. For instance, You want it to check for X and Y flipped tiles but not rotations.)

The idea:1 convert bitmap to 64 colors2 convert bitmap to chr3 removes duplicates(chr)4 make nametable(pal...) from bitmap and chr

Is it right?

I was looking for more of a generalized tool since I'm not working on NES at the moment. It wouldn't need to be platform specific at all. Ideally it would handle various pixel bit depths correctly. It just takes a bitmap of whatever depth and covert it to a tile set bitmap and an array (in C, in text, in asm, whatever).

There was one made for the GBA that did this (can't find it on my computer anymore, tho... nor remember the name.) and since it worked with 4bpp tiles, SNES and PCE tilemaps could be made as well. It did have a bug where it dropped about 3 tiles per tilemap, but it served its purpose well enough.

I use my GFX converter for such a job, it supports 4 or 8 bit BMP files and can generate just tiles, tiles arranged for sprites and as optimized image file that holds a tilemap and tiles with dupes removed. Made for MD but can do SMS/GG too (and possibly other machines too with some adjustments).No user interface nor command line, only takes a configuration file with parameters laid out. No error checks so there will be some possibly spectacular fails on bad input

Retro Graphics Toolkit should be able to do that see viewtopic.php?f=21&t=9894If you want a custom tile bit-depth or size that will be available soon. Also with Lua scripting you will have lots of possibilities to do what you want.

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